[Bioperl-l] not recognizing hsp in a hit

pageski Cynthia.Page at Colorado.EDU
Fri Apr 15 15:18:14 UTC 2011

Thanks for your responses, I am using blat version 34 and used -blast output

Steve Chervitz-2 wrote:
> On Thu, Apr 7, 2011 at 2:28 AM, Dave Messina
> <David.Messina at sbc.su.se>wrote:
>> I should also say: I wouldn't be surprised if the blast-style output that
>> Blat produces is slightly nonstandard and causes our parser to make
>> mistakes. By the way, which version of Blat are you using?
>> It looks like Jim Kent has taken Blat at least semi-commercial:
>> http://www.kentinformatics.com/products.html
>> If there's a new version of blat, I don't think BioPerl has seen it yet.
>> Can anyone confirm or deny recent Blat output format changes?
> It's not recent, but this might possibly be the culprit:
> blat quirk in -blast output mode:
> https://lists.soe.ucsc.edu/pipermail/genome/2008-April/016211.html
> Steve
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